FunGAP: Fungal Genome Annotation Pipeline using evidence-based gene model evaluation.
作者： Byoungnam Min , Igor V Grigoriev , In-Geol Choi
DOI: 10.1093/BIOINFORMATICS/BTX353
关键词:
摘要: Motivation: Successful genome analysis depends on the quality of gene prediction. Although fungal sequencing and assembly have become trivial, its annotation procedure has not been standardized yet. Results: FunGAP predicts protein-coding genes in a assembly. To attain high-quality models, this program runs multiple predictors, evaluates all predicted genes, assembles models that are highly supported by homology to known sequences. do this, we built scoring function estimate congruency each model based protein or domain homology. Availability implementation: is written Python script available GitHub (https://github.com/CompSynBioLab-KoreaUniv/FunGAP). This software freely only for noncommercial users. Contact: igchoi@korea.ac.kr Supplementary information:Supplementary data at Bioinformatics online.
oup.com
elsevier.com
sci-hub.se 参考文章(8)
M. Stanke, O. Keller, I. Gunduz, A. Hayes, S. Waack, B. Morgenstern, AUGUSTUS: ab initio prediction of alternative transcripts Nucleic Acids Research. ,vol. 34, pp. 435- 439 ,(2006) , 10.1093/NAR/GKL200
Grzegorz M. Boratyn, Christiam Camacho, Peter S. Cooper, George Coulouris, Amelia Fong, Ning Ma, Thomas L. Madden, Wayne T. Matten, Scott D. McGinnis, Yuri Merezhuk, Yan Raytselis, Eric W. Sayers, Tao Tao, Jian Ye, Irena Zaretskaya, BLAST: a more efficient report with usability improvements Nucleic Acids Research. ,vol. 41, pp. 29- 33 ,(2013) , 10.1093/NAR/GKT282
P. Jones, D. Binns, H.-Y. Chang, M. Fraser, W. Li, C. McAnulla, H. McWilliam, J. Maslen, A. Mitchell, G. Nuka, S. Pesseat, A. F. Quinn, A. Sangrador-Vegas, M. Scheremetjew, S.-Y. Yong, R. Lopez, S. Hunter, InterProScan 5: genome-scale protein function classification Bioinformatics. ,vol. 30, pp. 1236- 1240 ,(2014) , 10.1093/BIOINFORMATICS/BTU031
Felipe A. Simão, Robert M. Waterhouse, Panagiotis Ioannidis, Evgenia V. Kriventseva, Evgeny M. Zdobnov, BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs Bioinformatics. ,vol. 31, pp. 3210- 3212 ,(2015) , 10.1093/BIOINFORMATICS/BTV351
Alexander V Lukashin, Mark Borodovsky, GeneMark.hmm: New solutions for gene finding Nucleic Acids Research. ,vol. 26, pp. 1107- 1115 ,(1998) , 10.1093/NAR/26.4.1107
Brandi L Cantarel, Ian Korf, Sofia MC Robb, Genis Parra, Eric Ross, Barry Moore, Carson Holt, Alejandro Sánchez Alvarado, Mark Yandell, MAKER: An easy-to-use annotation pipeline designed for emerging model organism genomes Genome Research. ,vol. 18, pp. 188- 196 ,(2007) , 10.1101/GR.6743907
Katharina J. Hoff, Simone Lange, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke, BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS Bioinformatics. ,vol. 32, pp. 767- 769 ,(2016) , 10.1093/BIOINFORMATICS/BTV661
Robert D. Finn, Penelope Coggill, Ruth Y. Eberhardt, Sean R. Eddy, Jaina Mistry, Alex L. Mitchell, Simon C. Potter, Marco Punta, Matloob Qureshi, Amaia Sangrador-Vegas, Gustavo A. Salazar, John Tate, Alex Bateman, The Pfam protein families database: towards a more sustainable future Nucleic Acids Research. ,vol. 44, pp. 279- 285 ,(2016) , 10.1093/NAR/GKV1344